2P5W
Crystal structures of high affinity human T-cell receptors bound to pMHC reveal native diagonal binding geometry
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | 293 | 85 MM HEPES, 8.5% ISO-PROPANOL, 17% PEG4000, 15% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.46 | 50.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 74.59 | α = 90 |
| b = 52.325 | β = 98.13 |
| c = 118.932 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | MIRROR | 2004-06-17 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SRS BEAMLINE PX14.2 | SRS | PX14.2 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
| 1 | 2.2 | 24.805 | 99.3 | 0.145 | 0.145 | 4.3 | 3.8 | 46229 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.2 | 2.32 | 99.5 | 0.51 | 0.51 | 1.5 | 3.8 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2F53 | 2.2 | 24.8 | 43884 | 2332 | 99.26 | 0.16941 | 0.16532 | 0.24456 | RANDOM | 14.825 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| 0.19 | 2.2 | 0.8 | -0.36 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 24.07 |
| r_scangle_it | 9.998 |
| r_dihedral_angle_3_deg | 8.655 |
| r_scbond_it | 7.846 |
| r_dihedral_angle_4_deg | 7.687 |
| r_mcangle_it | 5.386 |
| r_mcbond_it | 4.324 |
| r_dihedral_angle_1_deg | 2.031 |
| r_angle_refined_deg | 1.711 |
| r_mcbond_other | 1.372 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6556 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 675 |
| Heterogen Atoms | 113 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| AMoRE | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
